An integrated framework for microbiome reconstruction from sequencing data. It leverages tools like Kraken2 for taxonomic classification and combines cell barcodes, UMIs, and k-mer-based quantification to reconstruct microbial signals. Designed for both bulk and single-cell sequencing data, the package enables taxonomic and quantitative profiling of microbial communities.
You can install mire from CRAN using:
# install.packages("pak")
pak::pak("mire")Alternatively, install the development version from r-universe with:
pak::repo_add("https://yunuuuu.r-universe.dev")
pak::pak("mire")or from GitHub with:
pak::pak("Yunuuuu/mire")You must also install kraken2.
sessionInfo()
#> R version 4.4.2 (2024-10-31)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.1 LTS
#>
#> Matrix products: default
#> BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libmkl_rt.so; LAPACK version 3.8.0
#>
#> locale:
#> [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
#> [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
#> [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
#> [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
#>
#> time zone: Asia/Shanghai
#> tzcode source: system (glibc)
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> loaded via a namespace (and not attached):
#> [1] compiler_4.4.2 fastmap_1.2.0 cli_3.6.5 tools_4.4.2
#> [5] htmltools_0.5.8.1 yaml_2.3.10 rmarkdown_2.29 knitr_1.50
#> [9] xfun_0.52 digest_0.6.37 rlang_1.1.6 evaluate_1.0.3